RetrogeneDB ID: retro_cjac_3878

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285708.1:3308..4784(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SUPV3L1
• Ensembl ID: ENSCJAG00000012937
• Aliases: None
• Description: None

Sequence

>retro_cjac_3878
CAAATGATTAGAGATCCAGCTAGAGGATGGGCCTGGTCCAGAGCACTTCTAGGACTCTGTGCTGAAGAAATTCATTTGTG
TGGAGAACCTGCCGCTATTGACCTGGTGACAGAGCTCATGTTCACAATGGGAGAGGAAGTGGAGGTTCAAGACTATAAGA
GGCTTACCCCTATCTCTGTGCTGGACCATGCACTAGAATCTTTAGATAACCTTCAGCCTGGGGACTGCATTGTCTGTTTT
GGCAAGTATGGTATTTATTCTGTGAGTCGGCAGATTGAAATTCGGGCATTAGAATCAGCCATTATATATGGCAGTCTCCC
ACCTGGGACCAAATTTGCTCAAGCAAAAAAGTTTAATGATCCCAATGACCCATGCAAAATCTTGGTTGCTACAGATGCAA
TTGGCATGGGTCTTAATTTGAGCATAAGGAGAATTATTTTTTACTCCTTTATAAAGCCCAGTATCAATTAAAAGGGAGAG
AAAGACATAGAACCAATCACAACCTCTCAGGCCCTGCAGATTGCTGGCAGAGCTGGCAGATTCAGCTCGCAGTTTAAAGA
AGGAGAGGTTACAACAAAGAACTGTGAAGATCTCAGTTTATTAAAGGAAATTTTGAATAGGCCTGTGGATCCCATAAGGG
CAGCTGGTCTTCATCCAACTGCTGAGCAGATTGAAATGTTTTCCTACCATCTCCCTGATACAACGCTTTCCAATCTCATT
GATATTTTTGTAGACTTTTCACAAGTTGACGGGCAGTATTTTGTCTGCAATATGGATGATTTTAAATTTTCTGCAGAGTT
GATCCAGCATGTTCCATTAAGTCTGCAAGTGAGGTATATTTTCTGCATGGCCCCTATCAACAAGAAGTAGCCTTTTGTGT
GCTCTTCCCTGTTACACTTTGCCAGGCAGTATAGCAGGAATGAGCCTCTGACCTTTGCATGGTTACGCCAACACATCAAA
TGGCCTTTATTTCCACCTAAGAATATTAAAGACCTCATGGATCTTGAAGCTATCCATGATGTCTTGGATCTTTACCTGTG
GCTAAGCTACTGATTTATGGATATGTTTCCAGGTGCCAGCATTATTCGAGATCTCCAGAAAGAACTAGATGCTATTATCC
AAGATGGTGTGCACAATATCACTAAATTGATTAAAATTTCTGAGACACGTAAGCTGTTGAATTTGGAGAGCTTTCCATCA
GACAGCCAGTCACGATTATCAGGAGTCTGAAGGAGCCAAGCTAGAAGGGCACGCGGCACCAAAGCTCTAGGAAGTAAAGC
TGCTGAGCCACCCAACCCCAATGCCGGAGAGCTGTCCCTTGCTATCAGATTGGTGCAGCAAGGACTCCTCACTCCAAATA
TGCTGAAACAGCTAGAAAAAGAGTGGATGACACAACAAATTGAACGTAACAGAGAAAGAGTAGCATCTGAGACTCATTCA
AAAGGAACGAGAAGAAAGAAGGAACCTGATTCAGAT

Alignment

ORF - retro_cjac_3878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 62.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMIRDPARGWAWTRALLGLCAEEIHLCGEPAAIDLVTELMFTTGEEVEVQDYKRLTPISVLDRALESLDN
          QMIRDPARGWAW.RALLGLCAEEIHLCGEPAAIDLVTELMFT.GEEVEVQDYKRLTPISVLD.ALESLDN
Retrocopy QMIRDPARGWAWSRALLGLCAEEIHLCGEPAAIDLVTELMFTMGEEVEVQDYKRLTPISVLDHALESLDN

Parental  LRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPDDPCKILVATDAIGMGLNL
          L.PGDCIVCF.K..IYSVSRQIEIR.LESA.IYGSLPPGTK.AQAKKFNDP.DPCKILVATDAIGMGLNL
Retrocopy LQPGDCIVCFGKYGIYSVSRQIEIRALESAIIYGSLPPGTKFAQAKKFNDPNDPCKILVATDAIGMGLNL

Parental  SIRRIIFYSLIKPSINEKGEKEIEPITTSQALQIAGRAGRFSSQFKEGEVTTMNREDLSLLKEILNRPVD
          SIRRIIFYS.IKPSIN.KGEK.IEPITTSQALQIAGRAGRFSSQFKEGEVTT.N.EDLSLLKEILNRPVD
Retrocopy SIRRIIFYSFIKPSIN*KGEKDIEPITTSQALQIAGRAGRFSSQFKEGEVTTKNCEDLSLLKEILNRPVD

Parental  PIRAAGLHPTAEQIEMFAYHLPDTTLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYV
          PIRAAGLHPTAEQIEMF.YHLPDTTLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQH.PLSL.VRY.
Retrocopy PIRAAGLHPTAEQIEMFSYHLPDTTLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHVPLSLQVRYI

Parental  FCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRHIKWPLLPPKNIKDLVDLEAIHDVLDLYLWLSY
          FC.APINKK.PFVCSSLL.FARQYSRNEPLTFAWLR.HIKWPL.PPKNIKDL.DLEAIHDVLDLYLWLSY
Retrocopy FCMAPINKK*PFVCSSLLHFARQYSRNEPLTFAWLRQHIKWPLFPPKNIKDLMDLEAIHDVLDLYLWLSY

Parental  RFMDMFPDASIIRDLQKELDAIIQDGVHNITKLIKISETRKLLNLESFPSERQSRLSGVLRSQARRARGT
          .FMDMFP.ASIIRDLQKELDAIIQDGVHNITKLIKISETRKLLNLESFPS..QSRLSGV.RSQARRARGT
Retrocopy *FMDMFPGASIIRDLQKELDAIIQDGVHNITKLIKISETRKLLNLESFPSDSQSRLSGV*RSQARRARGT

Parental  KALGSKAAEPPSPDARELSLASRLVQQGLLTPDMLKQLEKEWMTQQIERNRERTESETHSKGTRRKKEPD
          KALGSKAAEPP.P.A.ELSLA.RLVQQGLLTP.MLKQLEKEWMTQQIERNRER..SETHSKGTRRKKEPD
Retrocopy KALGSKAAEPPNPNAGELSLAIRLVQQGLLTPNMLKQLEKEWMTQQIERNRERVASETHSKGTRRKKEPD

Parental  SD
          SD
Retrocopy SD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.18 RPM	9.98 RPM
SRP051959_heart	0.18 RPM	18.52 RPM
SRP051959_kidney	0.00 RPM	20.34 RPM
SRP051959_liver	0.04 RPM	21.42 RPM
SRP051959_lung	0.02 RPM	13.97 RPM
SRP051959_lymph_node	0.18 RPM	13.65 RPM
SRP051959_skeletal_muscle	0.04 RPM	26.14 RPM
SRP051959_spleen	0.02 RPM	13.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3878 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012937	1 retrocopy	retro_cjac_3878 ,